Some theists believe that good and evil are simply what God says they are, but a large number think that God commands things because they are good, not that they are good because it's what God commands. Therefore, a lot of theists have a value system that is independent of God, and there's no reason why atheists can't have similar value systems. (FWIW, I'm a utilitarian, which is a moral belief that's completely independent of any God.)
As an example, suppose God commanded that you get some children and torture and violate them in all sorts of ways until they were physically crippled and emotionally ruined, then throw them into the gutter. Is this something you could understand happening? You can say God would never do that, but why do you say that?